Contacts of the strand formed by residues 79 - 91 (chain C) in PDB entry 2V16
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C THR* 3.5 32.3 - - + -
73C LEU 3.2 5.6 - - - +
74C ARG* 3.6 23.1 - - + +
75C TYR 4.6 0.3 + - - -
78C GLY* 1.3 73.5 + - - -
80C VAL* 1.3 72.5 + - - +
81C SER* 5.4 1.1 - - - +
108C PRO* 2.7 34.4 - - - +
112C PHE* 3.9 0.9 - - - -
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Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C TRP* 4.1 23.8 - - + +
72C THR* 3.9 2.3 - - - +
73C LEU* 3.1 44.4 + - + +
75C TYR* 4.3 4.3 - - + -
79C THR* 1.3 85.9 - - - +
81C SER* 1.2 60.3 + - - +
104C VAL* 3.8 23.8 - - + -
106C GLU* 3.4 8.7 - - - +
107C MET* 4.9 3.1 - - + -
108C PRO* 4.3 2.2 - - + -
112C PHE* 3.1 35.7 - - + -
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Residues in contact with SER 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C GLU* 6.0 0.3 - - - +
71C LEU 3.4 3.8 + - - -
72C THR* 2.4 34.9 + - - +
73C LEU* 6.0 0.2 - - - -
79C THR* 5.7 1.3 - - - -
80C VAL* 1.2 73.4 - - - +
82C GLY* 1.4 58.6 + - - +
104C VAL* 3.4 8.8 - - - +
105C THR* 3.3 13.8 + - - -
106C GLU* 3.0 45.4 + - - +
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Residues in contact with GLY 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C GLU* 3.6 13.3 + - - +
71C LEU* 2.7 28.8 + - - +
81C SER* 1.4 77.5 - - - +
83C PHE* 1.3 67.8 + - - +
102C GLY* 6.2 0.2 - - - -
103C GLU 3.4 12.6 - - - -
104C VAL* 3.9 1.6 - - - -
105C THR* 3.8 13.0 - - - -
106C GLU* 5.1 0.9 + - - -
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Residues in contact with PHE 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C SER* 4.2 1.6 - - - -
44C LYS* 3.5 36.3 - - + -
64C TYR* 5.3 5.8 - - - -
66C HIS* 5.3 6.1 - + - -
68C GLY* 3.7 22.0 - - - +
69C THR 3.1 14.8 - - - +
70C GLU* 4.3 8.1 - - - +
71C LEU* 4.6 3.0 - - - +
82C GLY* 1.3 75.7 - - - +
84C LEU* 1.3 76.4 - - - +
85C SER* 4.3 4.5 - - - -
102C GLY* 3.2 3.1 - - - -
103C GLU* 2.7 68.8 + - + +
105C THR* 3.9 18.8 - - + -
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASN* 5.5 1.1 - - - +
67C ASN* 3.5 21.3 + - + +
68C GLY 2.9 22.2 + - - -
69C THR* 2.8 31.6 + - - +
70C GLU 5.6 0.2 - - - +
71C LEU* 3.5 33.2 - - + -
83C PHE* 1.3 76.6 - - - +
85C SER* 1.3 67.8 + - - +
100C MET* 4.7 13.0 - - - -
101C PHE* 3.3 23.1 - - - +
131C GLY* 5.8 3.4 - - - +
133C VAL* 4.3 22.7 - - + -
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Residues in contact with SER 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C TYR* 3.6 22.8 - - - -
65C LYS 3.8 4.3 - - - -
67C ASN* 4.5 5.4 - - - +
83C PHE* 4.0 6.0 + - - -
84C LEU* 1.3 78.1 - - - +
86C GLN* 1.4 58.2 + - - +
100C MET* 3.2 11.9 - - - +
101C PHE* 2.8 49.3 + - - -
103C GLU* 2.8 28.7 + - - +
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Residues in contact with GLN 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C SER 4.7 0.4 + - - -
64C TYR* 3.3 1.7 - - - -
65C LYS* 2.7 74.2 + - + +
85C SER* 1.4 73.1 - - - +
87C ASP* 1.3 61.7 - - - +
97C THR* 3.4 38.2 + - - +
99C GLN 3.3 11.2 - - - +
100C MET* 3.4 27.9 - - + +
101C PHE* 4.1 1.1 - - - -
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Residues in contact with ASP 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ILE* 3.9 5.2 - - + -
21C GLY* 3.3 16.1 - - - -
56C PHE* 3.7 5.5 - - + -
61C SER* 2.8 29.8 + - - -
63C SER* 2.6 32.7 + - - -
64C TYR* 3.3 16.5 + - + +
86C GLN* 1.3 76.5 - - - +
88C ILE* 1.3 79.8 + - - +
89C ILE* 4.6 1.0 - - - +
97C THR* 3.4 3.5 - - - -
99C GLN* 3.0 26.1 + - - +
101C PHE* 3.8 20.0 - - + -
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C GLY 3.7 0.4 - - - +
20C ILE* 3.4 2.3 - - - -
21C GLY* 2.8 31.2 + - - +
22C THR* 3.2 27.4 - - + +
63C SER* 4.5 10.1 - - - +
87C ASP* 1.3 87.2 + - - +
89C ILE* 1.3 57.4 + - - +
90C THR* 5.3 5.8 - - - +
95C THR* 4.4 16.8 - - + +
96C VAL 3.4 10.3 - - - +
97C THR* 3.0 28.5 - - + +
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Residues in contact with ILE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 4.0 20.0 - - + -
19C GLY 3.4 4.7 - - - +
20C ILE* 3.4 29.8 - - + -
38C VAL* 3.9 19.3 - - + -
87C ASP 4.6 0.7 - - - +
88C ILE* 1.3 60.2 - - - +
90C THR* 1.3 77.1 + - - +
91C VAL* 4.2 0.4 - - + -
95C THR* 3.5 1.9 - - - -
96C VAL* 2.7 41.5 + - + +
99C GLN* 3.9 23.3 - - + -
101C PHE* 3.9 22.0 - - + -
136C ILE* 3.9 17.9 - - + -
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Residues in contact with THR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU 4.3 0.5 - - - +
18C ILE* 3.4 8.3 - - - +
19C GLY* 3.0 42.3 + - - -
24C PRO* 5.0 9.4 - - - +
88C ILE* 5.0 6.4 + - - +
89C ILE* 1.3 80.4 + - - +
91C VAL* 1.3 61.3 + - - +
92C GLY 4.0 1.3 + - - -
93C GLY* 5.0 8.5 - - - +
94C ILE 3.5 11.2 - - - +
95C THR* 3.3 23.2 + - - +
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C VAL* 4.8 4.7 - - + -
17C GLU 4.8 1.3 - - - -
18C ILE* 3.8 25.6 - - + -
31C PHE* 4.6 12.3 - - + -
89C ILE* 4.2 1.8 - - + +
90C THR* 1.3 74.2 - - - +
92C GLY* 1.3 63.2 + - - +
93C GLY 3.3 0.7 - - - -
94C ILE* 2.9 26.0 + - + +
96C VAL* 5.2 2.0 - - + -
121C VAL* 5.5 2.5 - - + -
136C ILE* 3.6 31.4 - - + -
140C ILE* 4.0 27.6 - - + -
167C LEU* 4.6 11.8 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il